# Elucidating the Evolution of Microbial Genes, Genomes and Communities

> **NIH NIH R35** · UNIVERSITY OF TEXAS AT AUSTIN · 2024 · $419,910

## Abstract

Project Summary / Abstract
Genomic methods have catalyzed a renaissance in the way that microorganisms are being studied.
Previously, most knowledge of microbial processes and functions was obtained from a very limited
number of tractable genetic systems. In contrast, current focus on microbiomes has shifted emphasis
towards understanding a broad diversity of lifeforms that are only known from sequences and whose
functions are inferred by homology to known or characterized organisms. Among the primary goals of
our research program is to bridge these two approaches by adopting genomic, computational and
experimental methods that directly test the roles, functions and adaptations of the non-model
organisms that predominate in microbiomes. The first of the three Subject Areas proceeds from our
findings that not only is there a high degree of host species-specificity in the contents of gut
microbiomes but certain bacterial lineages have been co-diversifying with their hosts over millions of
years. We will investigate how this co-diversification has progressed within the human population, and
determine if and how these co-diversifying bacteria interact with hosts by testing their adaptive role in a
dietary trait that is subject to strong selection in humans. We will also gain insights into the evolutionary
history of the human microbiome by analyzing the new resolved strain-level variation detected in
microbiome in a population genetics framework. The second Subject Area asks how new genes and
functions originate in bacterial genomes. Most models of new gene formation are based on the
duplication and modification of existing genetic information, and ignore the more fundamental question
about how completely new genes can arise de novo. Whereas in eukaryotes, non-coding sequences
seem to serve as templates for de novo gene origination, in bacteria there is strong, though indirect,
evidence that phage may be the inventive source of new genes. The proposed research will determine
the mechanisms by which new genes originate by testing the functional relevance and beneficial effects
conferred by new viral sequences integrated into bacterial genomes. The third Subject Area proposes
to address several questions concerning the role of viruses in microbial communities using a newly
developed experimental system derived from viruses known previously only from metagenomic
sequences. This system will allow us to resolve issues relating to viral host ranges, lifestyles and
interactions—all questions that would remain as inferences, or wholly unanswered, if only genome
sequences are available. Finally, we our plan to define the limits of gene exchange among viruses both
to establish uniformity in their classification into meaningful biological units and to understand the
potential for strains with new etiologies, distributions, and host tropisms to emerge.

## Key facts

- **NIH application ID:** 10889014
- **Project number:** 5R35GM118038-09
- **Recipient organization:** UNIVERSITY OF TEXAS AT AUSTIN
- **Principal Investigator:** Howard Ochman
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $419,910
- **Award type:** 5
- **Project period:** 2016-08-01 → 2026-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10889014

## Citation

> US National Institutes of Health, RePORTER application 10889014, Elucidating the Evolution of Microbial Genes, Genomes and Communities (5R35GM118038-09). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10889014. Licensed CC0.

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